Course Home

Applied Structural Bioinformatics 6-9 September 2010

This page we will use to collect links to resources you might need during the course or later :)

Tutorials

• PyMOL
  
• Electrostatics
• Structure prediction
• WebNM@
• Amber peptide
• Amber HNE
  

Presentations

• Introduction
• PDB
• Electrostatics
• Structure prediction
  
• Summary
• Dynamics WebNM@
  
• Molecular Dynamics
  

Setup details

The course computers have been installed with default MPI packages from the UIB IT-dept. Most newer user accounts will be aware of where to find this, but some older university accounts have been set up with a different login shell, namely tcsh. The command

printenv | grep SHELL

will reveal which shell you are using. If the output is SHELL=/bin/tcsh then you need to set some additional envirionment variables. Download this file:

• mpi-tcsh-variables

and execute the following command in the terminal you want to run mpi programs in (from the directory where you downloaded the file):

source mpi-tcsh-variables

 The lines in the file can also be appended to the end of your .cshrc file in your home directory, and these necessary changes will be done for you everytime you open a terminal.  (If you use this file on your own computer (not IT dept managed) note that the paths to the mpiprograms set in the file may differ).